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‎Data_science/DataMining/DataMining/Clustering/HDBSCAN/Distance/CosineSimilarity.vb‎

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#Region "Microsoft.VisualBasic::8ecb413476b369d318c83ea59d28f6bc, Data_science\DataMining\DataMining\Clustering\HDBSCAN\Distance\CosineSimilarity.vb"
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' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
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' along with this program. If not, see <http://www.gnu.org/licenses/>.
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' /********************************************************************************/
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' Summaries:
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' Code Statistics:
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' Total Lines: 108
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' Code Lines: 86 (79.63%)
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' Comment Lines: 4 (3.70%)
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' - Xml Docs: 75.00%
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'
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' Blank Lines: 18 (16.67%)
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' File Size: 5.30 KB
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' Class CosineSimilarity
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'
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' Constructor: (+1 Overloads) Sub New
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' Function: (+2 Overloads) CalculateAndCacheMagnitude, (+2 Overloads) ComputeDistance, GetMostCommonDistanceValueForSparseMatrix
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'
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'
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' /********************************************************************************/
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' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
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' along with this program. If not, see <http://www.gnu.org/licenses/>.
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' /********************************************************************************/
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' Summaries:
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' Code Statistics:
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' Total Lines: 108
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' Code Lines: 86 (79.63%)
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' Comment Lines: 4 (3.70%)
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' - Xml Docs: 75.00%
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'
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' Blank Lines: 18 (16.67%)
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' File Size: 5.30 KB
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' Class CosineSimilarity
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'
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' Constructor: (+1 Overloads) Sub New
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' Function: (+2 Overloads) CalculateAndCacheMagnitude, (+2 Overloads) ComputeDistance, GetMostCommonDistanceValueForSparseMatrix
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'
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'
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' /********************************************************************************/
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#End Region
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Imports System
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Imports System.Collections.Concurrent
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Imports System.Collections.Generic
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Imports stdNum = System.Math
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Imports std = System.Math
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Namespace HDBSCAN.Distance
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''' <summary>
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''' Computes cosine similarity between two points, d = 1 - ((X*Y) / (||X||*||Y||))
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''' </summary>
@@ -116,7 +115,7 @@ Namespace HDBSCAN.Distance
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i += 1
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End While
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Dim lComputeDistance = stdNum.Max(0, 1 - dotProduct / stdNum.Sqrt(magnitudeOne * magnitudeTwo))
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Dim lComputeDistance = std.Max(0, 1 - dotProduct / std.Sqrt(magnitudeOne * magnitudeTwo))
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Return lComputeDistance
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End Function
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@@ -137,15 +136,15 @@ Namespace HDBSCAN.Distance
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Next
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End If
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Return stdNum.Max(0, 1 - dotProduct / stdNum.Sqrt(magnitudeOne * magnitudeTwo))
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Return std.Max(0, 1 - dotProduct / std.Sqrt(magnitudeOne * magnitudeTwo))
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End Function
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Private Function CalculateAndCacheMagnitude(index As Integer, attributes As Dictionary(Of Integer, Integer)) As Double
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Dim hasValueValue As (hasValue As Boolean, value As Double) = Nothing
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hasValueValue = _tryGet(index)
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If hasValueValue.hasValue Then Return hasValueValue.value
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Dim magnitude = attributes.Keys.Sum(Function(i) stdNum.Pow(attributes(i), 2))
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Dim magnitude = attributes.Keys.Sum(Function(i) std.Pow(attributes(i), 2))
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_tryAdd(index, magnitude)
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Return magnitude
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End Function
@@ -155,7 +154,7 @@ Namespace HDBSCAN.Distance
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hasValueValue = _tryGet(index)
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If hasValueValue.hasValue Then Return hasValueValue.value
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Dim magnitude = attributes.Sum(Function(val) stdNum.Pow(val, 2))
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Dim magnitude = attributes.Sum(Function(val) std.Pow(val, 2))
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_tryAdd(index, magnitude)
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Return magnitude
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End Function

‎Data_science/DataMining/DataMining/Clustering/HDBSCAN/Distance/EuclideanDistance.vb‎

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#Region "Microsoft.VisualBasic::8a3335ba8382060b67ee54ecd9eb0a78, Data_science\DataMining\DataMining\Clustering\HDBSCAN\Distance\EuclideanDistance.vb"
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' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
26-
' along with this program. If not, see <http://www.gnu.org/licenses/>.
3+
' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
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' along with this program. If not, see <http://www.gnu.org/licenses/>.
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' /********************************************************************************/
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' /********************************************************************************/
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' Summaries:
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' Summaries:
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' Code Statistics:
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' Code Statistics:
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' Total Lines: 20
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' Code Lines: 15 (75.00%)
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' Comment Lines: 3 (15.00%)
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' - Xml Docs: 100.00%
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'
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' Blank Lines: 2 (10.00%)
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' File Size: 895 B
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' Total Lines: 20
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' Code Lines: 15 (75.00%)
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' Comment Lines: 3 (15.00%)
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' - Xml Docs: 100.00%
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'
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' Blank Lines: 2 (10.00%)
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' File Size: 895 B
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' Class EuclideanDistance
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'
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' Function: ComputeDistance
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'
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'
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' /********************************************************************************/
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' Class EuclideanDistance
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'
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' Function: ComputeDistance
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'
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'
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' /********************************************************************************/
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#End Region
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Imports stdNum = System.Math
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Imports std = System.Math
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Namespace HDBSCAN.Distance
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''' <summary>
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distance += (attributesOne(i) - attributesTwo(i)) * (attributesOne(i) - attributesTwo(i))
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i += 1
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End While
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Return stdNum.Sqrt(distance)
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Return std.Sqrt(distance)
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End Function
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End Class
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End Namespace

‎Data_science/DataMining/DataMining/Clustering/HDBSCAN/Distance/ManhattanDistance.vb‎

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#Region "Microsoft.VisualBasic::89ba23ef83e45034d62aad9f11bf22ae, Data_science\DataMining\DataMining\Clustering\HDBSCAN\Distance\ManhattanDistance.vb"
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' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
18-
' (at your option) any later version.
19-
'
20-
' This program is distributed in the hope that it will be useful,
21-
' but WITHOUT ANY WARRANTY; without even the implied warranty of
22-
' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23-
' GNU General Public License for more details.
24-
'
25-
' You should have received a copy of the GNU General Public License
26-
' along with this program. If not, see <http://www.gnu.org/licenses/>.
3+
' Author:
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'
5+
' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23+
' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
26+
' along with this program. If not, see <http://www.gnu.org/licenses/>.
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' /********************************************************************************/
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' /********************************************************************************/
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' Summaries:
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' Summaries:
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' Code Statistics:
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' Code Statistics:
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' Total Lines: 20
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' Code Lines: 15 (75.00%)
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' Comment Lines: 3 (15.00%)
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' - Xml Docs: 100.00%
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'
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' Blank Lines: 2 (10.00%)
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' File Size: 840 B
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' Total Lines: 20
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' Code Lines: 15 (75.00%)
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' Comment Lines: 3 (15.00%)
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' - Xml Docs: 100.00%
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'
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' Blank Lines: 2 (10.00%)
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' File Size: 840 B
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' Class ManhattanDistance
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'
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' Function: ComputeDistance
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'
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'
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' /********************************************************************************/
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' Class ManhattanDistance
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'
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' Function: ComputeDistance
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'
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'
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' /********************************************************************************/
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#End Region
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Imports stdNum = System.Math
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Imports std = System.Math
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Namespace HDBSCAN.Distance
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''' <summary>
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Dim i = 0
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While i < attributesOne.Length AndAlso i < attributesTwo.Length
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distance += stdNum.Abs(attributesOne(i) - attributesTwo(i))
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distance += std.Abs(attributesOne(i) - attributesTwo(i))
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i += 1
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End While
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Return distance

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